Performance uncertainty in medical image analysis: a large-scale investigation of confidence intervals

Performance uncertainty quantification is essential for reliable validation and eventual clinical translation of medical imaging artificial intelligence (AI). Confidence intervals (CIs) play a central role in this process by indicating how precise a reported performance estimate is. Yet, due to the limited amount of work examining CI behavior in medical imaging, the community remains largely unaware of how many diverse CI methods exist and how they behave in specific settings. The purpose of this study is to close this gap. To this end, we conducted a large-scale empirical analysis across a total of 24 segmentation and classification tasks, using 19 trained models per task group, a broad spectrum of commonly used performance metrics, multiple aggregation strategies, and several widely adopted CI methods. Reliability (coverage) and precision (width) of each CI method were estimated across all settings to characterize their dependence on study characteristics. Our analysis revealed five principal findings: 1) the sample size required for reliable CIs varies from a few dozens to several thousands of cases depending on study parameters; 2) CI behavior is strongly affected by the choice of performance metric; 3) aggregation strategy substantially influences the reliability of CIs, e.g. they require more observations for macro than for micro; 4) the machine learning problem (segmentation versus classification) modulates these effects; 5) different CI methods are not equally reliable and precise depending on the use case. These results form key components for the development of future guidelines on reporting performance uncertainty in medical imaging AI.

STARS: Shared-specific Translation and Alignment for missing-modality Remote Sensing Semantic Segmentation

Multimodal remote sensing technology significantly enhances the understanding of surface semantics by integrating heterogeneous data such as optical images, Synthetic Aperture Radar (SAR), and Digital Surface Models (DSM). However, in practical applications, the missing of modality data (e.g., optical or DSM) is a common and severe challenge, which leads to performance decline in traditional multimodal fusion models. Existing methods for addressing missing modalities still face limitations, including feature collapse and overly generalized recovered features. To address these issues, we propose \textbf{STARS} (\textbf{S}hared-specific \textbf{T}ranslation and \textbf{A}lignment for missing-modality \textbf{R}emote \textbf{S}ensing), a robust semantic segmentation framework for incomplete multimodal inputs. STARS is built on two key designs. First, we introduce an asymmetric alignment mechanism with bidirectional translation and stop-gradient, which effectively prevents feature collapse and reduces sensitivity to hyperparameters. Second, we propose a Pixel-level Semantic sampling Alignment (PSA) strategy that combines class-balanced pixel sampling with cross-modality semantic alignment loss, to mitigate alignment failures caused by severe class imbalance and improve minority-class recognition.

PAINT: Pathology-Aware Integrated Next-Scale Transformation for Virtual Immunohistochemistry

Virtual immunohistochemistry (IHC) aims to computationally synthesize molecular staining patterns from routine Hematoxylin and Eosin (H\&E) images, offering a cost-effective and tissue-efficient alternative to traditional physical staining. However, this task is particularly challenging: H\&E morphology provides ambiguous cues about protein expression, and similar tissue structures may correspond to distinct molecular states. Most existing methods focus on direct appearance synthesis to implicitly achieve cross-modal generation, often resulting in semantic inconsistencies due to insufficient structural priors. In this paper, we propose Pathology-Aware Integrated Next-Scale Transformation (PAINT), a visual autoregressive framework that reformulates the synthesis process as a structure-first conditional generation task. Unlike direct image translation, PAINT enforces a causal order by resolving molecular details conditioned on a global structural layout. Central to this approach is the introduction of a Spatial Structural Start Map (3S-Map), which grounds the autoregressive initialization in observed morphology, ensuring deterministic, spatially aligned synthesis. Experiments on the IHC4BC and MIST datasets demonstrate that PAINT outperforms state-of-the-art methods in structural fidelity and clinical downstream tasks, validating the potential of structure-guided autoregressive modeling.

PyHealth 2.0: A Comprehensive Open-Source Toolkit for Accessible and Reproducible Clinical Deep Learning

Difficulty replicating baselines, high computational costs, and required domain expertise create persistent barriers to clinical AI research. To address these challenges, we introduce PyHealth 2.0, an enhanced clinical deep learning toolkit that enables predictive modeling in as few as 7 lines of code. PyHealth 2.0 offers three key contributions: (1) a comprehensive toolkit addressing reproducibility and compatibility challenges by unifying 15+ datasets, 20+ clinical tasks, 25+ models, 5+ interpretability methods, and uncertainty quantification including conformal prediction within a single framework that supports diverse clinical data modalities - signals, imaging, and electronic health records - with translation of 5+ medical coding standards; (2) accessibility-focused design accommodating multimodal data and diverse computational resources with up to 39x faster processing and 20x lower memory usage, enabling work from 16GB laptops to production systems; and (3) an active open-source community of 400+ members lowering domain expertise barriers through extensive documentation, reproducible research contributions, and collaborations with academic health systems and industry partners, including multi-language support via RHealth. PyHealth 2.0 establishes an open-source foundation and community advancing accessible, reproducible healthcare AI. Available at pip install pyhealth.

Sim-to-Real Transfer via a Style-Identified Cycle Consistent Generative Adversarial Network: Zero-Shot Deployment on Robotic Manipulators through Visual Domain Adaptation

The sample efficiency challenge in Deep Reinforcement Learning (DRL) compromises its industrial adoption due to the high cost and time demands of real-world training. Virtual environments offer a cost-effective alternative for training DRL agents, but the transfer of learned policies to real setups is hindered by the sim-to-real gap. Achieving zero-shot transfer, where agents perform directly in real environments without additional tuning, is particularly desirable for its efficiency and practical value. This work proposes a novel domain adaptation approach relying on a Style-Identified Cycle Consistent Generative Adversarial Network (StyleID-CycleGAN or SICGAN), an original Cycle Consistent Generative Adversarial Network (CycleGAN) based model. SICGAN translates raw virtual observations into real-synthetic images, creating a hybrid domain for training DRL agents that combines virtual dynamics with real-like visual inputs. Following virtual training, the agent can be directly deployed, bypassing the need for real-world training. The pipeline is validated with two distinct industrial robots in the approaching phase of a pick-and-place operation. In virtual environments agents achieve success rates of 90 to 100\%, and real-world deployment confirms robust zero-shot transfer (i.e., without additional training in the physical environment) with accuracies above 95\% for most workspace regions. We use augmented reality targets to improve the evaluation process efficiency, and experimentally demonstrate that the agent successfully generalizes to real objects of varying colors and shapes, including LEGO\textsuperscript{\textregistered}~cubes and a mug. These results establish the proposed pipeline as an efficient, scalable solution to the sim-to-real problem.

ColorConceptBench: A Benchmark for Probabilistic Color-Concept Understanding in Text-to-Image Models

While text-to-image (T2I) models have advanced considerably, their capability to associate colors with implicit concepts remains underexplored. To address the gap, we introduce ColorConceptBench, a new human-annotated benchmark to systematically evaluate color-concept associations through the lens of probabilistic color distributions. ColorConceptBench moves beyond explicit color names or codes by probing how models translate 1,281 implicit color concepts using a foundation of 6,369 human annotations. Our evaluation of seven leading T2I models reveals that current models lack sensitivity to abstract semantics, and crucially, this limitation appears resistant to standard interventions (e.g., scaling and guidance). This demonstrates that achieving human-like color semantics requires more than larger models, but demands a fundamental shift in how models learn and represent implicit meaning.

InstructTime++: Time Series Classification with Multimodal Language Modeling via Implicit Feature Enhancement

Most existing time series classification methods adopt a discriminative paradigm that maps input sequences directly to one-hot encoded class labels. While effective, this paradigm struggles to incorporate contextual features and fails to capture semantic relationships among classes. To address these limitations, we propose InstructTime, a novel framework that reformulates time series classification as a multimodal generative task. Specifically, continuous numerical sequences, contextual textual features, and task instructions are treated as multimodal inputs, while class labels are generated as textual outputs by tuned language models. To bridge the modality gap, InstructTime introduces a time series discretization module that converts continuous sequences into discrete temporal tokens, together with an alignment projection layer and a generative self-supervised pre-training strategy to enhance cross-modal representation alignment. Building upon this framework, we further propose InstructTime++, which extends InstructTime by incorporating implicit feature modeling to compensate for the limited inductive bias of language models. InstructTime++ leverages specialized toolkits to mine informative implicit patterns from raw time series and contextual inputs, including statistical feature extraction and vision-language-based image captioning, and translates them into textual descriptions for seamless integration. Extensive experiments on multiple benchmark datasets demonstrate the superior performance of InstructTime++.

SoS: Analysis of Surface over Semantics in Multilingual Text-To-Image Generation

Text-to-image (T2I) models are increasingly employed by users worldwide. However, prior research has pointed to the high sensitivity of T2I towards particular input languages - when faced with languages other than English (i.e., different surface forms of the same prompt), T2I models often produce culturally stereotypical depictions, prioritizing the surface over the prompt's semantics. Yet a comprehensive analysis of this behavior, which we dub Surface-over-Semantics (SoS), is missing. We present the first analysis of T2I models' SoS tendencies. To this end, we create a set of prompts covering 171 cultural identities, translated into 14 languages, and use it to prompt seven T2I models. To quantify SoS tendencies across models, languages, and cultures, we introduce a novel measure and analyze how the tendencies we identify manifest visually. We show that all but one model exhibit strong surface-level tendency in at least two languages, with this effect intensifying across the layers of T2I text encoders. Moreover, these surface tendencies frequently correlate with stereotypical visual depictions.

Cross-Domain Object Detection Using Unsupervised Image Translation

Unsupervised domain adaptation for object detection addresses the adaption of detectors trained in a source domain to work accurately in an unseen target domain. Recently, methods approaching the alignment of the intermediate features proven to be promising, achieving state-of-the-art results. However, these methods are laborious to implement and hard to interpret. Although promising, there is still room for improvements to close the performance gap toward the upper-bound (when training with the target data). In this work, we propose a method to generate an artificial dataset in the target domain to train an object detector. We employed two unsupervised image translators (CycleGAN and an AdaIN-based model) using only annotated data from the source domain and non-annotated data from the target domain. Our key contributions are the proposal of a less complex yet more effective method that also has an improved interpretability. Results on real-world scenarios for autonomous driving show significant improvements, outperforming state-of-the-art methods in most cases, further closing the gap toward the upper-bound.

Sim2real Image Translation Enables Viewpoint-Robust Policies from Fixed-Camera Datasets

Vision-based policies for robot manipulation have achieved significant recent success, but are still brittle to distribution shifts such as camera viewpoint variations. Robot demonstration data is scarce and often lacks appropriate variation in camera viewpoints. Simulation offers a way to collect robot demonstrations at scale with comprehensive coverage of different viewpoints, but presents a visual sim2real challenge. To bridge this gap, we propose MANGO -- an unpaired image translation method with a novel segmentation-conditioned InfoNCE loss, a highly-regularized discriminator design, and a modified PatchNCE loss. We find that these elements are crucial for maintaining viewpoint consistency during sim2real translation. When training MANGO, we only require a small amount of fixed-camera data from the real world, but show that our method can generate diverse unseen viewpoints by translating simulated observations. In this domain, MANGO outperforms all other image translation methods we tested. Imitation-learning policies trained on data augmented by MANGO are able to achieve success rates as high as 60\% on views that the non-augmented policy fails completely on.